Improving the Automatic Classification of Brain MRI Acquisition Contrast with Machine Learning

Automated quantification of data acquired as part of an MRI exam requires identification of the specific acquisition of relevance to a particular analysis. This motivates the development of methods capable of reliably classifying MRI acquisitions according to their nominal contrast type, e.g., T1 weighted, T1 post-contrast, T2 weighted, T2-weighted FLAIR, proton-density weighted. Prior studies have investigated using imaging-based methods and DICOM metadata-based methods with success on cohorts of patients acquired as part of a clinical trial. This study compares the performance of these methods on heterogeneous clinical datasets acquired with many different scanners from many institutions. RF and CNN models were trained on metadata and pixel data, respectively. A combined RF model incorporated CNN logits from the pixel-based model together with metadata. Four cohorts were used for model development and evaluation: MS research (n = 11,106 series), MS clinical (n = 3244 series), glioma research (n = 612 series, test/validation only), and ADNI PTSD (n = 477 series, training only). Together, these cohorts represent a broad range of acquisition contexts (scanners, sequences, institutions) and subject pathologies. Pixel-based CNN and combined models achieved accuracies between 97 and 98% on the clinical MS cohort. Validation/test accuracies with the glioma cohort were 99.7% (metadata only) and 98.4 (CNN). Accurate and generalizable classification of MRI acquisition contrast types was demonstrated. Such methods are important for enabling automated data selection in high-throughput and big-data image analysis applications.